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gpertea / stringtie

Transcript assembly and quantification for RNA-Seq
MIT License
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Error running prepDE.py #302

Closed venuraherath closed 3 years ago

venuraherath commented 3 years ago

Hi ,

When I run prepDE.py job exit with the following error. I am using StringTie/2.1.4 with Python/2.7.18.

Traceback (most recent call last): File "/sw/eb/software/StringTie/2.1.4-GCC-9.3.0/bin/prepDE.py", line 58, in samples = [(i,glob.iglob(os.path.join(opts.input,i,"*.gtf")).next()) for i in next(os.walk(opts.input))[1] if re.search(opts.pattern,i)] StopIteration

I have a directory structure as follows

├── ballgown │   ├── PVX_2d_1 │   │   ├── e2t.ctab │   │   ├── e_data.ctab │   │   ├── i2t.ctab │   │   ├── i_data.ctab │   │   ├── PVX_2d_1.gtf │   │   └── t_data.ctab │   ├── PVX_2d_2 │   │   ├── e2t.ctab │   │   ├── e_data.ctab │   │   ├── i2t.ctab │   │   ├── i_data.ctab │   │   ├── PVX_2d_2.gtf │   │   └── t_data.ctab │   ├── PVX_2d_3 │   │   ├── e2t.ctab │   │   ├── e_data.ctab │   │   ├── i2t.ctab │   │   ├── i_data.ctab │   │   ├── PVX_2d_3.gtf │   │   └── t_data.ctab

Can you help me in this regard? Thanks in advance.